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RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages

Virologica Sinica 2024年第1期39卷 156-168页

作者： Changqiao You Shuai Jiang Yunyun Ding Shunxing Ye Xiaoxiao Zou Hongming Zhang Zeqi Li Fenglin Chen Yongliang Li Xingyi Ge Xinhong Guo College of Biology Hunan UniversityChangsha410082China College of Bioscience and Biotechnology Hunan Agricultural UniversityChangsha410128China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

关键词： RNA barcode segments SARS-CoV-2 variants and related lineages HCoVs Genetic tests Complete genome sequences

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CsABF3-activated CsSUT1 pathway is implicated in pre-harvest water deficit inducing sucrose accumulation in citrus fruit

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Horticultural Plant Journal 2024年第1期10卷 103-114页

作者： Xiaochuan Ma Yuanyuan Chang Feifei Li Junfeng Yang Li Ye Tie Zhou Yan Jin Ling Sheng Xiaopeng Lu College of Horticulture Hunan Agricultural UniversityChangshaHunan 410128China National Center for Citrus Improvement ChangshaHunan 410128China Institute of Horticulture Hunan Academy of Agricultural ScienceChangshaHunan 410125China

Pre-harvest water deficit(PHWD)plays an important role in sugar accumulation of citrus fruit.However,the mechanism is not known well.Here,it was confirmed that PHWD promoted sucrose accumulation of citrus fruit,but had limited effect on fructose,glucose and total acid.A sucrose transporter,Cs SUT1,which localizes to the plasma membrane,was demonstrated to function in sucrose transport induced by PHWD.Compared to wild-type,Cs SUT1 overexpression in citrus calli stimulated sucrose,fructose and glucose accumulation,while its silencing in juice sacs reduced sucrose accumulation.Increased sugar accumulation in transgenic lines enhanced plant drought tolerance,and resulted in decreased electrolyte leakage,malondialdehyde and hydrogen peroxide contents,as well as increased superoxide dismutase activity and proline contents.An abscisic acid(ABA)-responsive transcription factor,Cs ABF3,was found with a same expression pattern with Cs SUT1 under PHWD.Yeast one-hybrid,electrophoretic mobility shift assay and dual-luciferase assays all revealed that Cs ABF3 directly bound with the Cs SUT1 promoter by ABA responsive elements.When Cs ABF3 was overexpressed in citrus calli,the sucrose,fructose and glucose concentration increased correspondingly.Further,transgenic studies demonstrated that Cs ABF3 could affect sucrose accumulation by regulating Cs SUT1.Overall,this study revealed a regulation of Cs ABF3 promoting Cs SUT1 expression and sucrose accumulation in response to PHWD.Our results provide a detail insight into the quality formation of citrus fruit.

关键词： Citrus Water deficit Pre-harvest Sucrose CsABF3 CsSUT1

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Flavonoids from mulberry leaves inhibit fat production and improve fatty acid distribution in adipose tissue in finishing pigs

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Animal Nutrition 2024年第1期16卷 147-157页

作者： Yingying Liu Yinglin Peng Chen Chen Huibo Ren Ji Zhu Yuan Deng Qingming Cui Xionggui Hu Jianhua He Huali Li Xinghui Zhu Yulong Yin Jun He Yi Xiao College of Animal Science and Technology Hunan Agricultural University hunan Institute of Animal and Veterinary Science Key Laboratory of Conservation and Genetic Analysis of Local Pig Breed Germplasm Resources College of Information and Intelligence Hunan Agricultural University Institute of Subtropical Agriculture Chinese Academy of Sciences

This study evaluated the effects of flavonoids from mulberry leaves (FML) on plasma biochemical indices,serum activities of lipid metabolism-related enzymes,fat morphology,fatty acid composition,and lipid metabolism in different adipose tissues of finishing pigs.We used 120 Chinese hybrid barrows of Berkshire and Bama mini-pigs with an average initial body weight of 45.11±4.23 kg.The pigs were randomly assigned to five treatment groups and fed a control diet based on corn,soybean meal,and wheat bran or a control diet supplemented with 0.02%,0.04%,0.08%,or 0.16%FML.Each experimental group had six replicates (pens),with four pigs per pen.After a 7-d adaptation period,the feeding trial was conducted for 58 d.Blood and adipose tissue samples were collected from 30 pigs (one pig per pen)at the end of the test.The results showed that FML supplementation significantly decreased the feed intake to body gain ratio,the plasma concentrations of total cholesterol and free fatty acids,and the serum activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (linear or quadratic effects,P<0.05),and decreased the plasma triglyceride concentration (quadratic,P=0.07).Increasing FML supplementation increased the average daily gain and serum activities of lipoprotein lipase (linear and quadratic effects,P<0.05) and adipose triglyceride lipase (linear,P<0.05).Dietary FML supplementation decreased the adipocyte area in the dorsal subcutaneous adipose (DSA) tissue of finishing pigs (linear,P=0.05) and increased the adipocyte area in the visceral adipose tissue (quadratic,P<0.01).Increasing FML supplementation decreased the C20:1 content in DSA,abdominal subcutaneous adipose,and visceral adipose tissues of finishing pigs (P<0.05) and increased the C18:3n3 and n-3 PUFA contents(P<0.05).The lipid metabolism genes were regulated by the PPARγ-LXRa-ABCA1 signaling pathway,and their expressions differed in different adipose tissues.These findings suggest that FML improved growth performance,regulated lipid metabolism,inhibited fat production

关键词： Finishing pig Mulberry leaf Flavonoid Lipid metabolism Fatty acid Lard

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Historical Changes and Multi-scenario Prediction of Land Use and Terrestrial Ecosystem Carbon Storage in China

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Chinese Geographical Science 2024年第3期34卷 487-503页

作者： AN Yue TAN Xuelan REN Hui LI Yinqi ZHOU Zhou College of Resources Hunan Agricultural UniversityChangsha 410128China School of Geographic Science Hunan Normal UniversityChangsha 410081China

Terrestrial carbon storage(CS)plays a crucial role in achieving carbon balance and mitigating global climate change.This study employs the Shared Socioeconomic Pathways and Representative Concentration Pathways(SSPs-RCPs)published by the Intergovernmental Panel on Climate Change(IPCC)and incorporates the Policy Control Scenario(PCS)regulated by China’s land management policies.The Future Land Use Simulation(FLUS)model is employed to generate a 1 km resolution land use/cover change(LUCC)dataset for China in 2030 and 2060.Based on the carbon density dataset of China’s terrestrial ecosystems,the study analyses CS changes and their relationship with land use changes spanning from 1990 to 2060.The findings indicate that the quantitative changes in land use in China from 1990 to 2020 are characterised by a reduction in the area proportion of cropland and grassland,along with an increase in the impervious surface and forest area.This changing trend is projected to continue under the PCS from 2020 to 2060.Under the SSPs-RCPs scenario,the proportion of cropland and impervious surface predominantly increases,while the proportions of forest and grassland continuously decrease.Carbon loss in China’s carbon storage from 1990 to 2020 amounted to 0.53×10^(12)kg,primarily due to the reduced area of cropland and grassland.In the SSPs-RCPs scenario,more significant carbon loss occurs,reaching a peak of8.07×10^(12)kg in the SSP4-RCP3.4 scenario.Carbon loss is mainly concentrated in the southeastern coastal area and the Beijing-TianjinHebei(BTH)region of China,with urbanisation and deforestation identified as the primary drivers.In the future,it is advisable to enhance the protection of forests and grassland while stabilising cropland areas and improving the intensity of urban land.These research findings offer valuable data support for China’s land management policy,land space optimisation,and the achievement of dual-carbon targets.

关键词： land use change Future Land Use Simulation(FLUS)model carbon storage carbon density dataset land use scenario China

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Betulinic acid protects against ovarian impairment by decreasing F-2 toxin-induced oxidative stress and inflammation associated with the downregulation of p38 expression in mice

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Food Science and Human Wellness 2024年第3期13卷 1292-1302页

作者： Li Kong Xinyu Gao Lijuan Zhu Xing Lin You Huang Chunlin Huang Wenjiang Yang Yazhi Chen Haoqiang Zhao Jing Wu Zhihang Yuan Jin’e Yi hunan Engineering Research Center of Livestock and Poultry Health Care College of Veterinary MedicineHunan Agricultural UniversityChangsha 410128China

F-2 toxin is an estrogenic mycotoxin that causes reproductive disorders in animals.Betulinic acid(BA)is a natural pentacyclic lupane-structure triterpenoid that has diverse pharmacological activities.In this study,the antioxidative and anti-inflammatory effects of BA and its underlying mechanism are explored in F-2 toxin-triggered mouse ovarian damage.We found that BA alleviated the F-2 toxin-induced ovarian impairment by stimulating follicle growth,reducing inflammatory cell infiltration,repairing damaged mitochondria and endoplasmic reticulum.Simultaneously,BA not only reversed F-2 toxin-induced reduction of follicle stimulating hormone(FSH)and luteinizing hormone(LH)levels in the serum,but also restrained the protein expression of the estrogen receptors a(ERa)and ERβ.Moreover,BA restored the balance of F-2 toxin-induced ovarian redox system disorders.Subsequently,we found that 0.25 mg/kg BA played an anti-inflammatory role in the F-2 toxin-induced ovarian impairment by decreasing interleukin-1β(IL-1β).IL-6,and tumor necrosis factor-α(TNF-α)mRNA expression,as well as inhibiting p38 protein expression.These data demonstrated that BA exerts its protective effect on F-2 toxin-induced ovarian oxidative impairment and inflammation by inhibiting p38 expression,which implies a natural product-based medicine to ameliorate F-2 toxin-caused female reproductive toxicity and provides a detoxifying method for food contaminated by mycotoxin.

关键词： Betulinic acid F-2 toxin Ovarian damage p38 MAPK signaling pathway

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Junshanyinzhen tea extract prevents obesity by regulating gut microbiota and metabolic endotoxemia in high-fat diet fed rats

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Food Science and Human Wellness 2024年第4期13卷 2036-2047页

作者： Jian Ouyang Xiuping Li Changwei Liu Danmin Lu Jie Ouyang Fang Zhou Qi Liu Jianan Huang Zhonghua Liu Key Laboratory of Tea Science of Ministry of Education Hunan Agricultural UniversityChangsha 410128China National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals Hunan Agricultural UniversityChangsha 410128China Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients Hunan Agricultural UniversityChangsha 410128China Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops Ministry of Agriculture and Rural AffairsHunan Agricultural UniversityChangsha 410128China

Obesity is associated with gut dysbiosis and metabolic endotoxin.Junshanyinzhen tea extract(JSTE)reduced fat accumulation and body weight in obese mice.However,the effects and mechanism of JSTE in preventing obesity were unclear.Therefore,we used different doses of JSTE(75,150 and 300 mg/(kg·day))to evaluate the effect on high-fat diet(HFD)-induced rats under 8 weeks of intervention.Here,our results showed that JSTE could significantly reduce body weight gain,blood lipid levels and fat accumulation,improve fatty damage in liver tissue(P<0.05).In addition,JSTE increased the expression of intestinal tight junction proteins(P<0.05),relieved metabolic endotoxemia(P<0.05)and chronic low-grade inflammation in HFD rats.Sequencing of fecal samples showed that JSTE could effectively reverse the microbial diversity and the ratio of Firmicutes to Bacteroidetes to normal levels in HFD-fed rats.Desulfovibrioceae and Erysipelotrichaceae,which are positively related to obesity,were decreased by JSTE intervention(P<0.05).while Bifidobacteriaceae,Bacteroidaceae,Akkermansia,and Clostridium,which are negatively related to obesity,were increased.Together,these results suggested that JSTE might effectively prevent obesity by modulating gut microbiota dysbiosis,intestinal barrier dysfunction,metabolic endotoxemia and chronic low-grade infl ammation in HFD-induced rats.

关键词： Junshanyinzhen tea Obesity Gut microbiota Gut barrier function Metabolic endotoxemia

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Polysaccharides of Aspergillus cristatus attenuate obesity by regulating gut microbiota and gut microbiota-related metabolites

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Food Science and Human Wellness 2024年第3期13卷 1513-1530页

作者： Mingzhi Zhu Bohao Shang Fang Zhou Yong Yuan Feiyan Yin Jin Cao Jianan Huang Kunbo Wang Xin Zeng Maiquan Li Zhonghua Liu College of Horticulture Hunan Agricultural UniversityChangsha 410128China College of Life Sciences Huaibei Normal UniversityHuaibei 235000China hunan Tea Group Co. Ltd.Changsha 410128China School of Food Science and Technology Hunan Agricultural UniversityChangsha 410128China

Golden-flower fungus,the only dominant microorganism determining the Fu-brick tea quality through fermentation and the important microbe in Liupao tea,is considered a potential probiotic fungus based on its anti-obesity effect.However,the classification of golden-flower fungi is still controversial;the anti-obesity effect of golden-flower fungus polysaccharides remains unknown.In this study,we identify a golden-flower strain as Aspergillus cristatus based on morphological characteristics and multigene phylogeny analysis,which resolves the controversy of classification.Moreover,we find A.cristatus polysaccharides(ACPS)attenuate obesity in rats.ACPS modulate gut bacterial composition.in which Akkermansia,Akkermansia muciniphila,Bacteroides,Romboutsia,Blautia,and Desulfovibrio are considered the core microbes regulated by ACPS.ACPS increase fecal total short-chain fatty acid content and serum,hepatic,and fecal total bile acid content.Furthermore,ACPS-induced gut microbiota alteration plays a causal role in the protection from obesity,according to a fecal transplantation experiment.Thus,ACPS ameliorate obesity by regulating gut microbiota and gut microbiota-related metabolites.

关键词： Golden-flower fungus Aspergillus cristatus Polysaccharides Obesity Gut microbiota

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Leucine regulates lipid metabolism in adipose tissue through adipokine-mTOR-SIRT1 signaling pathway and bile acid—microbe axis in a finishing pig model

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Animal Nutrition 2024年第1期16卷 158-173页

作者： Yunju Yin Saiming Gong Mengmeng Han Jingzun Wang Hanjing Shi Xianji Jiang Liu Guo Yehui Duan Qiuping Guo Qinghua Chen Fengna Li Key Laboratory of Agro-ecological Processes in Subtropical Region Institute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessHunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production College of Animal Science and Technology Hunan Agricultural University College of Modern agricultural Sciences University of Chinese Academy of Sciences College of Life Science and Engineering Northwest Minzu University

This study was conducted to explore the regulatory mechanism of leucine (Leu) on lipid metabolism of finishing pigs.Twenty-four Duroc×Landrace×Large cross pigs with an average body weight of68.33±0.97 kg were randomly allocated into 3 treatment groups with 8 replicates per group (1 pig per replicate).The dietary treatments were as follows:control group (CON),0.25%Leu group and 0.50%Leu group.The experimental period was 42 d.The results showed as follows.(1) Compared with the CON,0.25%and 0.50%Leu increased (P<0.01) the average daily gain (ADG),while the average backfat thickness (ABT) and the ratio of feed intake to body weight gain (F:G ratio) were decreased (P<0.05).(2)In the 0.25%Leu group,the relative mRNA expression levels of sterol regulatory element binding protein-1c (SREBP1c),recombinant fatty acid transport protein 1 (FATP1),chemerin and peroxisome proliferatoractivated receptor γ (PPARγ) were decreased but the level of fatty acid binding protein 4 (FABP4) and fatty acid translocase (FAT/CD36) were increased in backfat tissue.In the 0.25%Leu group,the protein levels of p-Rictor,p-Raptor,p-eIF4E-binding protein 1 (p-4EBP1),p-silent mating type information regulator 2homolog 1 (p-SIRT1) and acetylation ribosome s6 protein kinase 1 (Ac—S6K1) were increased (P<0.05).(3) Compared to the CON,the diversity of gut microbiota in the 0.25%Leu group was increased.Principal component analysis showed that the relative abundance of Bacteroidetes,Lactobacillus and Desulfovibrio was higher in the 0.25%Leu group than the CON,but the relative abundance of Firmicutes,Treponema and Shigella was lower than in the CON (P<0.05).(4) Four different metabolites were screened out from the serum of finishing pigs including allolithocholic acid (alloLCA),isolithocholic acid (isoLCA),ursodeoxycholic acid (UDCA) and hyodeoxycholic acid (HDCA),which correlate to various degrees with the above microorganisms.In conclusion,Leu could promote adipose tissue lipolysis of finishing pigs through the mTOR-SIRT1 signaling pathway,and S6K1 is a

关键词： Leu Lipid metabolism Gut microbiota Bile acid

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Identification and effective regulation of scarb1 gene involved in pigmentation change in autotetraploid Carassius auratus

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Zoological Research 2024年第2期45卷 381-397页

作者： Xi-Dan Xu Yue Zhou Chong-Qing Wang Xu Huang Kun Zhang Xiao-Wei Xu Li-Wen He Xin-Yue Zhang Xin-Zhu Fu Ming Ma Qin-Bo Qin Shao-Jun Liu State Key Laboratory of Developmental Biology of Freshwater Fish Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education MinistryCollege of Life SciencesHunan Normal UniversityChangshaHunan 410081China Nansha-South China agricultural university Fishery Research Institute GuangzhouGuangdong 511458China hunan Yuelu Mountain Science and Technology Co.Ltd.for Aquatic Breeding ChangshaHunan 410081China College of Chemistry and Chemical Engineering Hunan Normal UniversityChangshaHunan 410081China

The autotetraploid Carassius auratus(4nRR,4n=200,RRRR)is derived from whole-genome duplication of Carassius auratus red var.(RCC,2n=100,RR).In the current study,we demonstrated that chromatophores and pigment changes directly caused the coloration and variation of 4nRR skin(red in RCC,brownish-yellow in4nRR).To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR,we performed transcriptome profiling and molecular functional verification in RCC and 4nRR.Results revealed that scarb1,associated with carotenoid metabolism,underwent significant down-regulation in 4nRR.Efficient editing of this candidate pigment gene provided clear evidence of its significant role in RCC coloration.Subsequently,we identified four divergent scarb1 homeologs in 4nRR:two original scarb1 homeologs from RCC and two duplicated ones.Notably,three of these homeologs possessed two highly conserved alleles,exhibiting biased and allelespecific expression in the skin.Remarkably,after precise editing of both the original and duplicated scarb1homeologs and/or alleles,4nRR individuals,whether singly or multiply mutated,displayed a transition from brownishyellow skin to a cyan-gray phenotype.Concurrently,the proportional areas of the cyan-gray regions displayed a gene-dose correlation.These findings illustrate the subfunctionalization of duplicated scarb1,with all scarb1genes synergistically and equally contributing to the pigmentation of 4nRR.This is the first report concerning the functional differentiation of duplicated homeologs in an autopolyploidfish,substantiallyenrichingour understanding of coloration formation and change within this group of organisms.

关键词： Autopolyploidization Coloration change scarb1 Functional differentiation Genetic changes

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Changes in Leaf Stomatal Properties in Rice with the Growing Season

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Phyton-International Journal of Experimental Botany 2024年第4期93卷 807-817页

作者： Jiana Chen Fangbo Cao Min Huang Rice and Product Ecophysiology Key Laboratory of Ministry of Education for Crop Physiology and Molecular BiologyHunan Agricultural UniversityChangsha410128China National Engineering Research Center of Rice Hunan Agricultural UniversityChangsha410128China

Transplanting rice varieties grown in different seasons can lead to different yields due to different dry matterproduction. Early-season rice varieties transplanted in the late season can obtain high yields with short-growthduration and higher yields driven by higher dry matter production. To make clear the variations in dry matterproduction across seasons, four early-season rice varieties were chosen for late-season transplantation. The grainyield, dry matter accumulation, leaf photosynthetic, and leaf stomatal properties were studied. It was observedthat the average yields of these four varieties in the late season were 33% greater, despite a reduced growth periodof 13 days in comparison with the early season. Furthermore, there was a notable increase in both total and postheadingdry matter production during the late season. The leaf net photosynthetic rate, stomatal area, stomatalwidth, and stomatal length were higher in the late season. Despite no significant difference in stomatal densitybetween seasons, strong positive linear relationships were observed between net photosynthetic rate and stomatalconductance, and between stomatal conductance and area. These relationships demonstrate that the increase ofthe stomatal width and length of the leaves in the late season leads to an increase in the stomatal area, therebyincreasing the stomatal conductance and enhancing the photosynthesis of the leaves. Consequently, this leads togreater dry matter production and a higher yield compared to the early season. Therefore, when breeding newhigh-yielding and short-growing varieties, the large stomatal area can be used as a reference index.

关键词： Photosynthesis rice stomatal properties season yield

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